Variant report

Variant	rs17499863
Chromosome Location	chr12:31860512-31860513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11051540	0.85[MKK][hapmap]
rs11051554	0.85[EUR][1000 genomes]
rs1150959	1.00[CHD][hapmap]
rs1150960	1.00[CHD][hapmap]
rs1150961	1.00[CHD][hapmap]
rs11829645	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835928	1.00[ASN][1000 genomes]
rs12302735	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302797	1.00[ASN][1000 genomes]
rs12303695	0.85[EUR][1000 genomes]
rs12316208	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318379	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259421	1.00[CHD][hapmap]
rs1259730	1.00[AFR][1000 genomes]
rs1267688	1.00[CHD][hapmap]
rs1677155	1.00[CHD][hapmap]
rs1677156	1.00[CHD][hapmap]
rs1677188	1.00[CHD][hapmap]
rs17500301	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2679501	1.00[CHD][hapmap]
rs34248310	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7955847	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967487	1.00[CHB][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7969600	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875746	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv898967	chr12:31858031-31899475	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31822600-31862000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:31822600-31874200	Weak transcription	Right Ventricle	heart
3	chr12:31827000-31871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:31837200-31865000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:31838600-31881000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:31839800-31871800	Weak transcription	Gastric	stomach
7	chr12:31840200-31861800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:31841600-31870000	Weak transcription	Pancreas	Pancrea
9	chr12:31844600-31871800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:31846400-31862400	Weak transcription	Aorta	Aorta
11	chr12:31846400-31871800	Weak transcription	Lung	lung
12	chr12:31849000-31880000	Weak transcription	Psoas Muscle	Psoas
13	chr12:31849600-31860800	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:31850800-31867600	Weak transcription	Brain Substantia Nigra	brain
15	chr12:31851000-31880800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:31851600-31860800	Weak transcription	Liver	Liver
17	chr12:31851600-31863200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:31852800-31861800	Weak transcription	Left Ventricle	heart
19	chr12:31852800-31871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:31852800-31879600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:31853000-31867200	Weak transcription	Brain Anterior Caudate	brain
22	chr12:31853400-31861800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr12:31854400-31862200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:31854600-31867400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:31854800-31867600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:31855000-31867600	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:31855400-31867600	Weak transcription	Stomach Mucosa	stomach
28	chr12:31858000-31867600	Weak transcription	A549	lung
29	chr12:31858000-31867800	Weak transcription	HUVEC	blood vessel
30	chr12:31858800-31863600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:31859000-31860600	Weak transcription	Thymus	Thymus
32	chr12:31859000-31871800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:31859400-31862000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:31859400-31862800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:31859600-31861000	ZNF genes & repeats	Fetal Brain Female	brain
36	chr12:31859800-31861800	Weak transcription	Fetal Stomach	stomach
37	chr12:31859800-31864400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:31860000-31860600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr12:31860000-31861000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr12:31860200-31860600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
41	chr12:31860200-31860600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:31860200-31860600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:31860200-31860600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
44	chr12:31860200-31860800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr12:31860200-31860800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:31860200-31860800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr12:31860200-31860800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
48	chr12:31860200-31860800	Strong transcription	Ovary	ovary
49	chr12:31860200-31860800	ZNF genes & repeats	Dnd41	blood
50	chr12:31860200-31861000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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